This document explores the healthy human virome, describing a complex relationship between viruses and their human hosts that can vary from mutualistic to pathogenic. It highlights that the majority of these viruses are bacteriophages found in the intestines, while some, like pegiviruses and herpesviruses, can replicate within human cells without causing disease. The review emphasizes the blurred lines between symbiotic and pathogenic viruses, which can shift based on the host’s health conditions and immune status.

1. The healthy human virome: from virus–host
symbiosis to disease
Eugene V Koonin1
, Valerian V Dolja2
and Mart Krupovic3
Viruses are ubiquitous, essential components of any
ecosystem, and of multicellular organism holobionts.
Numerous viruses cause acute infection, killing the host or
being cleared by immune system. In many other cases, viruses
coexist with the host as symbionts, either temporarily or for the
duration of the host’s life. Apparently, virus–host relationships
span the entire range from aggressive parasitism to mutualism.
Here we attempt to delineate the healthy human virome, that is,
the entirety of viruses that are present in a healthy human body.
The bulk of the healthy virome consists of bacteriophages
infecting bacteria in the intestine and other locations. However,
a variety of viruses, such as anelloviruses and herpesviruses,
and the numerous endogenous retroviruses, persist by
replicating in human cells, and these are our primary focus.
Crucially, the boundary between symbiotic and pathogenic
viruses is fluid such that members of the healthy virome can
become pathogens under changing conditions.
Addresses
1
National Center for Biotechnology Information, National Library of
Medicine, National Institutes of Health, Bethesda, MD, USA
2
Department of Botany and Plant Pathology, Oregon State University,
Corvallis, OR, USA
3
Archaeal Virology Unit, Institut Pasteur, Paris, France
Corresponding author: Koonin, Eugene V (koonin@ncbi.nlm.nih.gov)
Current Opinion in Virology 2021, 47:86–94
This review comes from a themed issue on The virome in health and
diseases
Edited by Kenneth Cadwell and David Wang
For complete overview about the section, refer The Virome in Health
and Diseases
Available online 27th February 2021
https://doi.org/10.1016/j.coviro.2021.02.002
1879-6257/ã 2021 Published by Elsevier B.V.
Introduction
Billions of years of perennial and ubiquitous co-evolution
between viruses and cells have produced a broad spec-
trum of virus–host interaction regimes, ranging from
aggressive antagonism to commensalism, whereby viruses
coexist with their hosts without harming them, at least, in
the short term, and even to mutualism when a virus is
beneficial and can be essential to the host [1–4]. The
relationship between a particular virus and its host can be
rarely, if ever, defined by a single regime. Rather, the
mode of virus–host interaction is a function of multiple
factors, including the environmental conditions, host and
virus population structure, the immunological status of
the host and many more.
Virus–host relationships that do not result in the demise
of the host cell have been described across the virosphere
[3,4]. Hence the concept of the ‘normal’ or ‘healthy’
virome, in principle, is applicable to any organism, includ-
ing humans. Indeed, although most of the best character-
ized human viruses cause acute infections and are associ-
ated with diseases, a healthy human organism is host to a
much greater variety of viruses [5,6,7
]. The substantial
majority of these infect bacteria that inhabit the human
intestine, but a number of viruses actually reproduce in
human cells without causing disease, at least, in the short
term.
In this brief review, we systematically discuss the healthy
human virome and emphasize that the boundary between
‘normal’ and pathogenic (that is, causally associated with
clinically manifested disease) viromes is blurred. Indeed,
the same virus can be either a symbiont (with either no
perceptible fitness effect on the host, that is, effectively, a
commensal, or with a beneficial effect) or a pathogen
depending on the conditions such as the health status and
developmental stage of the host. We further stress that
the current knowledge of symbiotic viruses lags far
behind that of the pathogenic viruses.
The healthy human phageome
The human intestine, by far the richest microbial habitat
in the body, contains about 1014
bacterial and archaeal
cells at any given moment [8
]. As many microbial com-
munities, the human microbiome hosts a broad variety of
viruses, in which tailed bacteriophages (class Caudovir-
icetes within the realm Duplodnaviria) comprise the over-
whelming majority [8
,9], albeit with a considerable con-
tribution by ssDNA phages of the families Microviridae
[10–12] and Inoviridae [13
] (realm Monodnaviria). Sys-
tematic metagenomics surveys of the human phageome
identify thousands of phages but show that relatively few
are common components of the healthy gut phageome.
Thus, one of the most detailed metagenomics analyses
resulted in the identification of only 23 phages that were
shared by 50% of the tested individuals [9]. Strikingly,
the most prevalent human-associated phage (and most
prominent component of the healthy human virome
altogether), the crAssphage, has been discovered only
through metagenomics [14]. This initial finding has been
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2. followed by the characterization of an expansive group of
crAss-like phages, also by metagenome analysis [15,16
].
Subsequently, some crAss-like phages have been grown
in cultures of the respective host bacteria, members of the
phylum Bacteroidetes [17,18]. Given the difficulty of
growing the human intestine-associated bacteria-phage
systems in the laboratory, the actual size and diversity of
the healthy human phageome remains to be discovered.
Importantly, substantial changes in the human phageome
have been associated with various diseases conditions,
including infection with human and simian immunodefi-
ciency viruses, and in some cases, the phageome pertur-
bation was, apparently, decoupled from the changes in
the microbiome [19–21].
Symbiotic viruses replicating in human cells
Over many decades, diverse viruses have been isolated
from healthy humans more or less by chance. In the last
few years, systematic surveys of the healthy human
virome became possible thanks to the advances of meta-
genomics [6,7
]. Below we briefly discuss the viruses that
have been shown, either by traditional virology
approaches or by metagenomics (Figure 1a), to be com-
monly present in healthy humans without causing appar-
ent disease, following the main divisions of the current
virus taxonomy [22
,23]. The key aspects of the
association of these viruses with the human organism
are summarized in Figure 1.
Realm Riboviria
Kingdom Orthornavira
The realm Riboviria consists of viruses with RNA gen-
omes as well as viruses with DNA genomes that employ
reverse transcription in their replication cycles. The
kingdom Orthornavira encompasses RNA viruses that
share homologous RNA-dependent RNA polymerases
(RdRP). Many RNA viruses have been isolated or
detected by metatranscriptomics in healthy humans
but few can be confidently identified as symbionts repli-
cating in human cells (Figure 1a).
Perhaps, the most notable apparent human symbionts
among the orthornaviruses are pegiviruses (family Flavi-
viridae) [24,25]. The prototypical pegivirus has been
initially tentatively identified as hepatitis G virus [26],
but no association with hepatitis has been subsequently
confirmed [27]. In the family tree of flavivirids, pegi-
viruses tightly cluster with hepaciviruses which include
hepatitis C virus (HCV), a major human pathogen [24,25].
However, unlike HCV, pegiviruses have not been linked
to any pathology. Pegivirus infection in humans is com-
mon, with the incidence of about 5%, and pegiviruses
Virus–host symbiosis in humans Koonin, Dolja and Krupovic 87
Figure 1
Nucleocytoviricota:
Phycodnaviridae,
Marseilleviridae,
Mimiviridae
Caudoviricetes:
‘Crassvirales’ , etc.
Microviridae
Picobirnaviridae
‘Statoviruses’
Genomoviridae
Virgaviridae
Herpesviridae
Healthy human virome
Bona fide human viruses Human-associated viruses
Polyomaviridae
Papillomaviridae
Flaviviridae:
Pegivirus
Retroviridae:
HERVs
Anelloviridae
Parvoviridae
Inoviridae
Smacoviridae
Healthy
adults
Bacteria
Hosts
Viral load,
pathogenicity
Disbalance/
Immunosuppression
(a) (b)
Immunity
stimulation
Immunity
stimulation,
protection
from cancer
Immunity stimulation,
antiviral protection
?
Immunity stimulation,
antiviral protection
Antiviral
protection?
Antiviral
protection
Fungi
Archaea
Plants
Protists
Riboviria
Monodnaviria
Duplodnaviria
Varidnaviria
Unassigned
Current Opinion in Virology
The healthy human virome. (a) Taxa of viruses found in healthy humans. Taxa of viruses replicating in human cells are shown on the left, whereas
those of viruses infecting human-associated microbes or associated with food sources are shown on the right (the actual or suspected hosts are
listed next to the corresponding taxa, with the uncertain assignments indicated with broken lines). Depicted virus taxa are represented with virion
structures which were retrieved from VIPERdb (viperdb.scripps.edu) or the Electron Microscopy Data Bank (https://www.ebi.ac.uk/pdbe/emdb/).
When the structure of a virus representing a particular taxon was not available, a structurally related member was chosen instead. Virus taxa are
colored according to their realm affiliation (the key is provided at the bottom). (b) Fluidity of the healthy human virome. The (potential) beneficial
effects of the healthy human virome are indicated next to the corresponding virus structures. Question marks denote uncertainty. Upon changes in
the health status/immunosuppression, viruses that cause asymptomatic infections or are beneficial in healthy individuals proliferate and can cause
diseases including severe ones. The figure illustrates the general tendency of increased virus load under immunosuppression/disease conditions
and should not be interpreted as a quantitative representation of the changes for any depicted group of viruses.
www.sciencedirect.com Current Opinion in Virology 2021, 47:86–94

3. readily grow in human cell cultures, leaving no doubt that
these are bona fide human viruses [25]. Notably, pegivirus
infection appears to be associated with benign clinical
outcome in AIDS patients [28,29] indicating that these
apparent viral symbionts of humans could benefit the host
via protection from other viruses.
A recent, intriguing addition to the human virome are
statoviruses (for STool-Associated TOmbus-like viruses)
that were originally identified in multiple metagenomes
from humans, macaques, cows and mice [30], followed by
detection in nasal-throat swabs of humans with acute
respiratory disease [31]. Although the actual hosts of
statoviruses remain unknown, RdRP phylogeny, where
statovirus RdRPs cluster with a variety of unclassified
tombus-like viruses from invertebrate holobionts (that is,
a host together with the entirety of associated symbionts
and parasites) [32], suggests that statoviruses are associ-
ated with either mammalian diet (e.g. plants) or, more
likely, some protist symbionts or parasites.
Another widespread group of putative members of the
healthy human virome are members of Picobirnaviridae.
Picobirnaviruses are commonly detected in mammalian,
includinghuman,intestinesandhavenotbeenconvincingly
linkedtoanydiseasesalthougharesuspectedtobeassociated
with diarrhea [33,34]. Picobirnaviruses have never been
grown in cell cultures, and their true hosts remain unknown.
The presence of highly conserved ribosome-binding sites
(Shine-Dalgarno sequences), which are a hallmark of
prokaryotic mRNAs, has led to the suggestion that picobir-
naviruses infect bacteria in mammalian microbiomes [35
].
In addition, certain food-derived plant viruses are present
in the human gastrointestinal tract and in feces, some-
times in substantial amounts. The list of such viruses is
topped by pepper mild mottle virus (PMMoV), a toba-
movirus commonly found in pepper, pepper-derived pro-
ducts and their consumers all over the world [36].
Remarkably, PMMoV retains infectivity after passing
through the human alimentary tract. Owing to its stability
and wide presence in human feces, PMMoV is used as a
surrogate marker of fecal contamination of water [37
].
However, given that there is no evidence of plant virus
replication in vertebrate cells, any substantial role of plant
viruses in human health is an extremely remote
possibility.
Kingdom Pararnavira
This virus kingdom includes viruses that employ reverse
transcription in their replication cycles. Over 3000 of
human endogenous retroviruses (HERVs) are integrated
into the host genome, comprising about 8% of human
DNA [38]. Accordingly, the HERVs play important and
diverse roles in human biology that cannot be discussed in
this brief review in any detail (for recent reviews, see
[39
,40,41,42
]). Most of the HERVs appear to descend
from ancient integration events so that the virus genes are
disrupted and rearranged. The legacy of these ancient
HERVs are genes encoding virus structural proteins (Gag
and Env) that have been recruited for a variety of physio-
logical functions [43], the best known being syncitins, the
placental trophoblast receptors [39
]. However, some
members of the youngest group of HERVs, known as
HERV-K or HML2, that are thought to have invaded the
human genome less than a million years ago form virus
particles, particularly, in early embryogenesis [44,45].
The HERV-K viruses, at least, are bona fide members
of the healthy human virome. Many of the other HERVs
are expressed as well and are implicated in a variety of
functions including modulation of innate immunity, even
though functional virus proteins are usually not produced
[46]. In particular, it has been reported that expression of
one of HERV-K suppresses the spread of invasive mela-
noma [47
]. However, potential associations between
HERVs and various diseases have been reported as well.
Thus, the relationship between the HERVs and the
human host is a typical symbiosis, with both beneficial
and potential deleterious effects on the host (Figure 1b).
Realm Monodnaviria
Realm Monodnaviria includes prokaryotic and eukaryotic
viruses which encode homologous replication initiation
endonucleases of the HUH superfamily or their inacti-
vated derivatives, as in the case of polyomaviruses and
papillomaviruses [22
,48]. In addition to phages of the
Microviridae and Inoviridae families mentioned above,
several other representatives of Monodnaviria have been
repeatedly identified as part of the healthy human vir-
ome. These include members of the families Parvovir-
idae, Genomoviridae, Smacoviridae, Papillomaviridae and
Polyomaviridae (Figure 1a). The actual hosts for
human-associated genomoviruses [49] and smacoviruses
[50] remain unknown but these viruses likely infect
human-associated microbes rather than humans directly.
Parvoviruses
Parvoviruses from several genera have been detected in
various samples from apparently healthy humans, includ-
ing human bocaviruses (HBoV; genus Bocaparvovirus),
adeno-associated viruses (AAVs; genus Dependoparvo-
virus), human parvovirus 4 (PARV4; genus Tetraparvo-
virus), parvovirus B19 (B19V; genus Erythroparvovirus)
and several protoparvoviruses (genus Protoparvovirus)
[51–54]. These viruses display highly variable cell tro-
pism and pathogenicity. For instance, AAVs and PARV4
can infect cells from multiple tissue types and are not
known to cause any disease. By contrast, HBoV is most
commonly found in the respiratory and gastrointestinal
tracts as well as in blood [55,56], and is associated with
acute respiratory symptoms, especially in children [57].
However, the direct role of HBoV as a pathogen remains
unclear. B19V invades red blood cell precursors in the
bone marrow and is commonly considered as a human
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4. pathogen causing a wide range of pathological conditions,
including the fifth disease in children, persistent anemia
in immunocompromised patients, transient aplastic cri-
ses, hydrops fetalis in pregnant women, and arthropathy
[52]. Yet, in healthy adults, B19V infections are largely
asymptomatic [58], with the prevalence of up to 25% in
healthy human skin biopsies [59]. Thus, B19V is a condi-
tional component of the ‘healthy’ human virome that can
turn into a pathogen in response to various factors
(Figure 1b).
Polyomaviruses and Papillomaviruses
Monodnaviria includes class Papovaviricetes that consists
of Polyomaviridae and Papillomaviridae, two families of
viruses with small (5–8 Kbps), circular dsDNA genomes
[60,61]. Papovaviruses are thought to have evolved from
parvoviruses [48], with polyomaviruses emerging in inver-
tebrates and co-evolving with animals for at least half a
billion years [62]. In humans, polyomaviruses lead a low-
profile life styles characterized by low propagation levels,
evasion of clearance by the immune system and asymp-
tomatic infections in immunocompetent individuals [60].
Apparently, human polyomaviruses have evolved mech-
anisms to limit their own reproduction levels in order to
establish persistent infections [63]. A poster child human
polyomavirus is John Cunningham virus (JCV) that estab-
lishes life-long latent infections [64]. The seroprevalence
of JCV and other human polyomaviruses in adults can
reach 90% or higher, with common coinfection by several
polyomaviruses that are transmitted through direct con-
tacts between humans or through contaminated objects.
Contrary to their name and the oncogenic potential of the
large T (tumor) antigen (the early virus protein involved
in genome replication) in experimental settings, most of
the human polyomaviruses are not oncogenic. The Mer-
kel cell polyomavirus is the only one that has been
convincingly identified as the etiological agent of the
eponymous carcinoma, a skin cancer caused by malignant
transformation of the skin neuroendocrine cells appar-
ently facilitated by virus genome integration into the host
chromosomes [60,65].
Papillomaviruses are the closest, albeit apparently some-
what ‘younger’ relatives of polyomaviruses that likely
emerged in vertebrates 350 mya, but their life style is
distinct. The majority of the 200 known human papil-
lomaviruses (HPVs) belong to Beta and Gamma types
(Betapapillomavirus and Gammapapillomavirus genera,
respectively), and cause unapparent productive infections
or low-grade disease of the skin or mucosal epithelium
(e.g. warts and condylomas) that are normally cleared by
the immune system [66,67]. The virus replication cycle is
tightly linked to epithelial differentiation and is orches-
trated by a regulatory network that involves coordination
between the cell cycle, virus DNA replication and tran-
scription, and RNA splicing [67,68]. Most of the infec-
tions by the ‘high-risk’, Alpha HPV types (HPV16 and
HPV18 being most prevalent; genus Alphapapillomavirus)
in women result in more prolonged cervical infections, 80-
90% of which are asymptomatic and are eventually
cleared by the immune system [66,67]. However, a small
fraction of such infections, primarily due to defects in the
immune response, progress to the formation of persistent
papillomas and, in a minority of cases, to cervical cancer.
This small fraction of HPV infections, nevertheless,
accounts for close to 100% of cervical cancers that affect
over 500 000 women annually [69]. On much rarer occa-
sions, the high-risk HPV also cause other types of carci-
nomas [70]. Carcinogenesis is a dead end for HPV
because transformed cells produce no infectious virus.
Therefore, despite the carcinogenic potential of high-risk
HPVs, by and large, these common components of human
virome should be considered symbionts, as demonstrated
by the protection from skin cancer caused by immunity to
ubiquitous skin-infecting HPVs [71
] (Figure 1b).
Anelloviruses
Members of the family Anelloviridae are among the most
enigmatic components of the healthy human virome,
both in terms of their evolutionary origin and the impact
on human health. Anelloviruses have small icosahedral
virions that encapsidate tiny (3–3.5 kb) circular ssDNA
genomes [72
], but unlike the ssDNA viruses in the
realm Monodnaviria, do not encode recognizable homo-
logs of the rolling circle replication endonuclease. More-
over, no homologs outside the family have been detected
for any of the anellovirus proteins. Hence, anelloviruses
are currently not included in the realm Monodnaviria and
their provenance remains unclear [22
,48]. The entire
human population is believed to be infected with anello-
viruses, and there is no convincing evidence of viral
clearance from infected individuals [72
,73]. The infec-
tions occur at an early age and so far have not been
convincingly associated with any disease. The virus load
appears to be controlled by the immune system because
virus levels increase with the level of host immunosup-
pression [74,75]. Asymptomatic anellovirus infections are
also common in other mammals [73,76–78], suggesting
extensive coevolution of anelloviruses with mammalian
hosts. Although the potential impact of anelloviruses on
human health remains a matter of debate, it has been
suggested that they positively influence human physiol-
ogy by shaping the immunity during early development
[72
]. Thus, anelloviruses might be the most ‘friendly’,
genuinely symbiotic component of the human virome.
Realm Duplodnaviria
The realm Duplodnaviria includes viruses with dsDNA
genomes that are encapsidated in icosahedral capsids
consisting of a distinct type of capsid protein,
displaying the HK97 fold (after the first phage for which
the capsid protein structure was solved), with the help of
the corresponding variety of packaging ATPase, known as
the terminase [22
]. This realm includes the bulk of the
Virus–host symbiosis in humans Koonin, Dolja and Krupovic 89
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5. viruses associated with the human microbiome, namely,
the numerous tailed bacteriophages, as well as a major
component of the virome associated with human cells, the
herpesviruses. Some of the human herpesviruses (Her-
pesviridae) infect a variety of cell types and cause life-long
latent infections [79]. Of the 9 human herpesviruses
identified so far, herpes simplex virus 1 (HSV1), human
cytomegalovirus (HCMV), Epstein-Barr virus (EBV) and
varicella zoster virus (VZV) are highly prevalent in the
human population. Depending on the geographic loca-
tion, socioeconomic status and, in the case of VZV,
vaccination levels, the incidence of these viruses reaches
up to 96% [80–82]. The health impact of these viruses (if
any) depends on the age and immune system status of the
infected person, with ethnicity, gender and genotype
being additional significant contributors.
The most stealthy of the human herpes viruses are
apparently EBV and HCMV. If acquired in childhood,
both of these viruses typically cause asymptomatic infec-
tions, mainly, in B-lymphocytes in the case of EBV [83] or
in several cell types in the case of HCMV [79]. Such silent
infections, however, even if not manifested in disease,
cause a range of effects at the molecular, cellular, tissue
and organism levels. In the case of EBV, the gene
expression pattern of infected B-cells is reprogrammed
[84] and the proportion of plasma cells in blood appears to
be increased [7
]. Major immunity stimulation effects, a
likely result of a balance reached over long virus–host co-
evolution process, are well established for HCMV. In
particular, 10% of the CD4+
and CD8+
T cells in
latently infected, otherwise healthy adults are HCMV-
specific. Likewise, HCMV causes expansion of adaptive
CD57+
natural killer (NK) cells targeting virus–infected
cells [85]. These powerful arms of the immune system,
however, fail to clear the virus due to its armament of
immunoevasins, HCMV-encoded proteins involved in
modulation of host immunity [86
]. Extensive immunity
stimulation in HCMV-seropositive individuals appears to
enhance responsiveness and protection against heterolo-
gous viruses rather than compromise host immunity
[86
]. These potentially positive effects notwithstand-
ing, damaging consequences of herpesvirus infections
appear to be fairly common and vary from mild illness
to a variety of life-threatening conditions. Thus, HCMV
congenital (in utero) infections that occur at up to 2% of
childbirths frequently cause neurodevelopmental defects
or leukemia [85]. At the other life extremity, in seniors,
HCMV seropositivity is associated with increased risks of
cancer, cardiovascular disease, and ultimately, mortality.
The delicate, life-long EBV-host balance arising from
most childhood infections is also fragile: if infection
occurs in even non-immunocompromised young adults,
it results in infectious mononucleosis (‘kissing disease’)
[87]. Similarly, EBV is etiologically linked to Hodgkin’s
and Burkitt’s lymphomas and nasopharyngeal carcinoma
which are common in Southern Chinese and Eskimo
people, as well as to a host of other diseases in immuno-
compromised individuals [83]. A different pathology pat-
tern is characteristic of VZV infections that cause varicella
(chickenpox) in children followed by prolonged latency
that, in about 15% cases, leads to virus reactivation in
elderly people with weakened immune control, causing
zoster (postherpetic neuralgia) [88].
The HSV1 infections exhibit another distinct pattern of
virus–host interactions. This virus is normally acquired in
childhood causing mainly oral infections; its seropreva-
lence varies from 70% in developed nations to 100% in
developing nations [81,89]. Upon infecting epithelial
cells, HSV1 is transmitted to axons and establishes life-
long latency in dorsal root ganglia that is periodically
manifested in reactivation leading to recurrent acute
infections or asymptomatic virus shedding. Similar to
other human herpesviruses, HSV1 efficiently evades
antiviral innate immune responses mediated by Toll-like
and other pathogen recognition receptors. The underly-
ing mechanisms of HSV1 immunoevasion involve multi-
ple virus proteins targeting diverse innate immunity
signaling pathways [90].
Thus, human herpesviruses display a striking variety of
cell tropisms and infection patterns that emerged over
long-term virus–human co-evolution and co-adaptation.
Some herpesviruses, in particular HCMV and EBV, can
reach a perfect balance with the human host and often
persist for the host’s lifetime without causing any pathol-
ogy. However, because of the complexity of virus–host
interactions that involve a variety of genetic, environ-
mental and socioeconomic factors, this balance is fragile
and can be broken in many situations resulting in mor-
bidity or even mortality (Figure 1b). Therefore,
herpesvirus–host co-existence that involves the majority
of the human population blurs the very concept of a
‘healthy human virome’.
Realm Varidnaviria
This realm includes a broad variety of viruses with
dsDNA genomes and icosahedral capsids built of protein
unrelated to the capsid proteins of duplodnaviruses [22
]. Unlike the members of Duplodnaviria, varidnaviruses
are minor components of the healthy human virome, at
best. Several intriguing reports have appeared on the
detection of large and giant viruses of the class Nucleocy-
toviricota in healthy humans [91]. Perhaps, the most
notable of these findings is the detection in human blood
of several members of Marseilleviridae one of which has
been reported to grow in T lymphocytes [92]. Addition-
ally, several viruses from both Marseilleviridae and Mimi-
viridae have been isolated from human stools or detected
in human-associated metagenomes [93]. Furthermore,
the presence of mimiviruses in peripheral blood mono-
nuclear cells of patients with atypical pneumonia has
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6. been reported, and a role for these viruses in the pneu-
monia pathogenesis has been suggested [94]. Unexpect-
edly, DNA of Acanthocystis turfacea chlorella virus 1, a
member of Phycodnaviridae, has been detected in nearly
half of the tested oropharyngeal samples from healthy
humans, and also has been reported to persist in mouse
macrophages [95]. However, so far, many of the reports on
the presence of members of Nucleocytoviricota in human
samples and, especially, their ability to replicate in human
cells have been disavowed in follow-up studies [96].
Thus, the status of these viruses as components of the
healthy human virome except, perhaps, as occasional
contaminants, remains dubious.
Conclusions
The healthy virome of any organism, and especially
humans, clearly, is an important component of the holo-
biont that makes a major contribution to the health status
of the host. However, the very concept of a healthy
virome is nebulous and fluid because it is virtually impos-
sible to ascertain that any virus would not cause disease
under any conditions. A strong case in point are the
herpesviruses that are nearly ubiquitous in the human
population, remaining symbionts in most individuals
most of the time, but consistently cause disease, in some
cases, devastating, in immunocompromised individuals.
Conversely, it appears plausible that any virus can
become beneficial to the host through protection from
other viruses, general stimulation of immunity as in the
striking case of b-HPV protecting human hosts from skin
cancer, or recruitment of virus genes for host functions.
The numerous HERVs integrated in the human genome
can be considered the paradigm of virus–host symbiosis.
Generally, there is no doubt that many viruses evolved
multiple mechanisms to manipulate the host innate and
adaptive immunity pathways, ensuring virus persistence
and controlling the damage to the host, as most conspic-
uously exemplified by the latent herpesviruses that are
virtually ubiquitous in the human population.
The healthy virome is obviously heterogeneous and
consists of 3 distinct components (Figure 1a): Firstly,
viruses that systematically enter the human organism,
primarily, with food, but do not replicate in humans;
secondly, viruses infecting prokaryotes and, possibly,
unicellular eukaryotes that comprise the healthy human
microbiome; and finally, viruses that actually replicate
and persist in human cells. With the advances of meta-
genomics, the human ‘microbiovirome’ has become a
subject of intense studies that continue bringing discov-
eries of new bacteriophage groups. In contrast, the ‘true’
healthy human virome is poorly understood, with many
questionable sightings of diverse viruses but little solid
evidence on persistence mechanisms. On the whole, and
in contrast to the disease-associated virome, the healthy
human virome appears to be dominated by DNA viruses,
in particular, anelloviruses and herpesviruses, that are
substantially more common than RNA viruses in healthy
humans. A thorough investigation of this component of
the healthy virome can be expected to enhance our
understanding of virus–host interactions and have major
implications for human health.
Conflict of interest statement
Nothing declared.
Acknowledgments
EVK is supported by the Intramural Research Program of the National
Institutes of Health (National Library of Medicine). MK was supported by
l’Agence Nationale de la Recherche grant ANR-20-CE20-0009.
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